Phylogenetic reconstruction of the evolutionary relationships between the members of the PPE protein family. The phylogenetic tree was constructed from the phylogenetic analyses done on the 180 aa N-terminal domains of the PPE proteins. The tree was rooted to the outgroup, Rv3873 (PPE68), shown to be the first PPE insertion into the ESAT-6 (esx) gene clusters (region 1). The gene highlighted in purple is present in ESAT-6 (esx) gene cluster region 1, genes highlighted in green are present in or have been previously shown to be duplicated from ESAT-6 (esx) gene cluster region 3 , the gene highlighted in blue is present in ESAT-6 (esx) gene cluster region 2, genes highlighted in red are present in or have been previously shown to be duplicated from ESAT-6 (esx) gene cluster region 5  and genes highlighted in yellow are members of the MPTR subfamily of the PPE family. Arrows indicate orthologues of genes present within the M. smegmatis genome sequence. Five sublineages (including the PPE-PPW, PPE-SVP and PPE-MPTR subfamilies) are indicated by Roman numerals.